Mr Cooper joined the company in 1989 and was appointed to the top job seven years ago.
Grant Cuff, chief executive of rival co-operative Alliance Group, is stepping down in December after nine years in the position and a 24-year tenure with the company. His successor is yet to be named.
There has also been much change recently in governance roles on the boards of both co-operatives.
Owen Poole, who was Mr Cuff's predecessor as chief executive, retired as chairman and an independent director of Alliance Group in September last year, North Canterbury farmer Murray Taggart replacing him as chairman.
Synlait Milk chairman Graeme Milne was appointed as an independent director last year, and Auckland businesswoman Vanessa Stoddart was appointed this year, while a replacement for recently retired John Waller is expected to be named soon.
Last year, Eoin Garden stood down from the board of Silver Fern Farms after a 15-year tenure, including five as chairman, with Rob Hewett taking over as chairman.
Barrister and accountant Jane Taylor was appointed as an independent director last year.
In last year's co-operative farmer-director elections, Alliance Group's Jason Miller was dumped and Don Morrison was elected.
At Silver Fern Farms, David Shaw was ousted and Richard Young and Dan Jex-Blake were elected.
Mr Morrison, Mr Young and Mr Jex-Blake were all previously involved with Meat Industry Excellence, a group that was established last year to seek industry reform.
This year's Alliance Group farmer-director elections will be interesting with incumbents John Lindsay and Dawn Sangster being challenged by Mandy Bell and Russell Drummond, who have both been backed by Meat Industry Excellence.
